Application of Natural Products in SARS-CoV-2

By Kamal Niaz

Application of Natural Products in SARS-CoV-2 examines the potential for natural products to treat COVID-19, bringing together the most recent research. SARS-CoV-2 is a novel disease H54 that is still being researched despite being globally prevalent. There are still few proven treatments, so repurposing existing drugs and treatments is essential. While there have been many articles published on the subject, this book is the first to bring together data and research on the topic. It includes information about molecular mechanism, dosage and safety profiles, and an essential resource for all scientists and researchers working to combat SARS-CoV-2.

• Collates known data and research on COVID-19 and natural products in a single and easy to find place
• Includes information about molecular mechanism, dosage and safety profiles
• Provides information from a diverse group of academics and industrial scientists

• Language: English
• Publisher: Academic Press
• Release date: Oct 20, 2022
• ISBN: 9780323950480

Book preview

Preface

Kamal Niaz

Phytochemicals are bioactive molecules found in plants that play vital roles in promoting health promotion and preventing illness. Since ancient times, humans have been using plant-based natural products as medicines against various ailments. Based on indigenous experience and traditions, the majority of current treatments are derived from plants. Since the outbreak of novel coronavirus, in which the first patient was linked to consumption of seafood at a market in Wuhan, Hubei Province, China, on 12th December 2019, no further cases have been reported. Later, on 11th February 2020, the World Health Organization (WHO) reported and named it Coronavirus Disease-19 (COVID-19), and the International Committee on Taxonomy of Viruses termed it as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Natural products and their constituents may play a significant role in the many phases of COVID-19 prevention, diagnosis, treatment, immunization, and research. With the help of this book, we combine the different technology techniques that will be extensively used during the global COVID-10 emergency. This book's research should be emphasized as the most recent literature on natural products utilized in the SARS-CoV-2 trial and as an appropriate reference. Phytochemicals are low-concentration secondary metabolites found in fruits and vegetables and are theorized to minimize the incidence of numerous pathological disorders. There are hundreds of phytochemicals in the diet, including flavonoids, phenolic acids, terpenes, and alkaloids, among many other types of compounds, that exhibit various bioactivities, such as antioxidant, antimutagenic, anticarcinogenic, antibacterial, and antiinflammatory properties. The research indicates that health advantages of eating fruits and vegetables are due to the additive and synergistic interactions between these phytocomponents. Consequently, minerals and bioactive substances found in fruits and vegetables should be favored over synthetic and costly dietary supplements.

This book will serve as a benchmark for academics, scientists, and health professionals as research continue to combat the COVID-19 pandemic and discover effective diagnostic tools. However, a single book proposal like this would not have been successful without the excitement and determination of publishers and scientists to take time from their hectic schedules and provide timely funding. We appreciate all the investigators who directly and indirectly participated in making this a reality. Additionally, I would like to thank my parents, brothers, sisters, and wife for the support they provided me while preparing this book.

Chapter 1

Natural products and SARS-CoV-2

Ihtisham Ul Haq¹, Fatima Fayyaz¹, Amna Shafqat¹, Abdul Basit², Firasat Hussain³, Israr Aziz¹, Zarak Imtiaz Khan¹, Amjad Islam Aqib⁴, Faisal Siddique³, Umair Younas⁵ and Kashif Rahim³,    ¹Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan,    ²Department of Microbiology, University of Jhang, Punjab, Pakistan,    ³Department of Microbiology, Faculty of Veterinary Science, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur, Punjab, Pakistan,    ⁴Department of Medicine, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur, Punjab, Pakistan,    ⁵Department of Livestock Management, Faculty of Animal Sciences and Production, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur, Punjab, Pakistan

Abstract

Natural products have been proven to be the source of many antiviral drugs in the past. History has a bunch of natural products used as traditional medicine, therapies, mixtures, and oils. However, there are many bioactive natural products that need to be evaluated against severe acute respiratory syndrome (SARS-CoV-2) to curb the ongoing pandemic. Several plants and fungal-derived natural products are extensively reported with antiviral activities against SARS-CoV-2. In vitro, preliminary study assays and computational studies revealed several antiviral drugs from natural fungal compounds, including cordycepin isolated from Cordyceps militaris fungi. Polyphenolic compounds isolated from the Broussonetia papyrifera plant showed promising antiviral activity against SARS CoV-2 in in silico studies. Two alkaloid compounds, 10-hydroxyusambarensine and cryptoquindoline isolated from African medicinal plants, inhibited the main protease (Mpro) of SARS CoV-2. At the start of the COVID-19 pandemic, FDA approved the emergency use of chloroquine against SARS CoV-2; chloroquine is a derivative of alkaloid. The development of modern technologies has streamlined the discovery of new drugs from natural products. Gas chromatography–mass spectrometry, infrared radiation, nuclear magnetic resonance, high-performance thin-layer chromatography, and high-performance liquid chromatography and other high output technologies should be available for the structural interpretation and distinguishability of prudent lead molecules

Keywords

SARS-CoV-2; natural products; history; plant-derived antiviral drugs; fungal; antiviral compounds

1.1 Introduction

In late December 2019, the Chinese population was diagnosed with a respiratory illness caused by an unidentified pathogen with pneumonia-like symptoms (Wu et al., 2020). Initially, the disease was believed to be pneumonia by healthcare officials; however, a thorough analysis of the patient throat sample by molecular-based diagnostic method detected a novel coronavirus. Hence, on 7 January, another pathogenic coronavirus was discovered; provisionally, it was named as novel coronavirus 2019 (nCoV-19) by the World Health Organization (WHO) (WHO, 2020a,b). Because of having genetic similarity with SARS-CoV, it was renamed as SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) by viral nomenclature scheme. SARS-CoV-2 belongs to the group of beta coronaviruses, which is enveloped and has genetic material present in the form of single-stranded RNA whose size is approximately 30 kb (Ayaz et al., 2021). The disease caused by SARS-CoV-2 was initially named viral pneumonia, but later, the WHO named it coronavirus disease-2019 (COVID-19) due to some symptoms of the lower respiratory tract like difficulty in breathing (WHO, 2020a,b). Other symptoms are fatigue, fever, coughing, sneezing, sputum production, and diarrhea reported in severe cases of systemic infection. Moreover, the patients also suffered from mental dissatisfaction, acute kidney failure, and dysfunction of various other organs (Wang et al., 2020a,b). The disease symptoms appear after 14 days of incubation and 4–5 days is the median. However, the incubation period fluctuated based on the patient health status and immunity, and it can be shorter in older persons and persons with a weak immune system. COVID-19 is transmitted through respiratory droplets (Jiang et al., 2020) very rapidly because of a more contagious temperament. Across China and the surrounding regions, the disease spread very rapidly, and on 13 January, Thailand reported the first COVID-19. Similarly, the first death case due to COVID-19 was reported in the Philippines, a resident of Wuhan, who developed the disease symptoms after arriving in the country, and after 1 week, he died (Hui et al., 2020). Comparatively, there is more virulence, pathogenicity, and contagiousness observed in newly emergent novel coronavirus, and the WHO declared COVID-19 a pandemic in the second week of March 2020 (WHO, 2020a,b). The emergence of COVID-19 revealed the hidden potential of coronaviruses and stressed the 21st century due to the lack of antiviral strategies for which various synthetic and natural products have been tested. The absence of powerful treatment for SARS-CoV-2 with pandemic potential accentuates the requirement for novel medications to treat coronaviruses. Various antiviral agents have been synthesized from natural products against several life-threatening infections, including SARS-CoV-2. Several natural sources are documented with the production of natural products with antiviral potential, but majorly plants and fungal-derived natural products are extensively reported with antiviral activities against SARS CoV-2 (Bhuiyan et al., 2020; Rao et al., 2020). In vitro assays and computational studies revealed several antiviral drugs from natural fungal compounds, including cordycepin isolated from Cordyceps militaris fungi. It produces a secondary metabolite cordycepin that has various biological functions, including antiviral property against SARS-CoV-2 (Verma, 2020). Fungal metabolites are a promising source for therapeutically important compounds that target the multiple marks of the viral lifecycle. Previously, promising antiviral activity had been documented against SARS CoV-2 by various polyphenol compounds isolated from the Broussonetia papyrifera plant, such as 3-methyl-2-enyl, 4-hydroxyisolonchocarpin, broussochalcone A, and 4,7-trihydroxyflavane. Main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) of SARS CoV-2 effectively inhibited viral activity with plant-derived polyphenols in in silico analysis (Bhuiyan et al., 2020). Moreover, the activity of Mpro of SARS CoV-2 has been terminated with flavonoid compounds in in silico studies. Two alkaloid compounds, 10-Hydroxyusambarensine and Cryptoquindoline isolated from African medicinal plants, inhibited the Mpro of SARS CoV and SARS CoV-2 both (Hussein et al., 2019). FDA approved the emergency use of chloroquine against this newly emergent coronavirus; chloroquine is a derivative of alkaloid. The discovery of new drugs from natural products has been streamlined by the development of modern technologies. Gas chromatography–mass spectrometry (GC–MS), infrared radiation (IR), nuclear magnetic resonance (NMR), high-performance thin-layer chromatography (HPTLC), and high-performance liquid chromatography (HPLC), and other high output technologies should be readily available for the structural interpretation of prudent lead molecules given by drug discovery studies (Krüger, 2020). It will help screen novel molecules by using computer programs and bioinformatics approaches in discovering new drugs from natural products.

This chapter illustrates the reported natural products-derived antiviral compounds, their sources, and efficacy against newly emergent SARS-CoV-2 and other human pathogenic viruses. The structural architecture of SARS-CoV-2, epidemiology, and diagnosis also have been focused on in this chapter. Previously reported natural products with antiviral potential are listed in Table 1.1.

Table 1.1

DENV-1, Dengue virus serotype-1; NDV, Newcastle disease virus; VSV, Vesicular Stomatitis Indiana virus.

1.2 Natural products and their role in traditional medicine

Natural product is broadly defined as any substance produced by a living organism as a byproduct of biotic materials and their metabolites. Living organisms produce two types of metabolites as natural products: primary metabolites, essential for an organism survival, and secondary metabolites, mainly not essential for survival but important for an organism immune system (Atanasov et al., 2015). Primary metabolites are important for intrinsic functions, including an organism development and metabolic processes such as building micro and macromolecules for sustaining life. On the other hand, secondary metabolites comprise extrinsic functions for organisms advantage in certain conditions. Hundreds of years of evolutionary processes structurally diversified the natural products into distinctive pharmacological and biological properties. In the recent era, modern drugs are synthesized using natural products as a startup to overcome side effects and enhance effectiveness (Krause and Tobin, 2013). Since existence, humans have relied on nature for their survival, either for food or for healthcare means. Natural products are primary and secondary metabolites produced by living organisms by metabolism and biosynthesis of macromolecules such as proteins and carbohydrates essential for the survival of living organisms (Dewick, 2002). Primary metabolites are used by living organisms and are essential, while secondary metabolites are not essential and are often produced to avoid environmental stresses (Colegate and Molyneux, 2007). Various processes such as photosynthesis, glycolysis, and the Krebs cycle are associated with the biosynthesis of secondary metabolites that give biosynthetic intermediates, also known as natural products. Shikimate pathways, acetate, and amino acids are used in the secondary metabolism, which leads to the production of shunt metabolites. Subsequently, it plays the role of intermediates in the production of secondary metabolites by alternate biosynthetic route, leading to the biosynthesis of secondary metabolites (Sarker et al., 2006). Compared to primary metabolites, secondary metabolites are more important for medicinal purposes. The plant-derived natural products used for medicinal purposes are synthesized by secondary metabolites, which are produced by biosynthetic intermediates of the core metabolic processes such as photosynthesis, Krebs cycle, and glycolysis (Dias et al., 2012). The abiotic factors, such as water, soil, air, chemicals, and radiations and biotic factors, such as bacteria, viruses, fungi, and algae, influence the biosynthetic pathways, which lead to the modifications in secondary metabolites and diversity in the product can be seen. A large number of medicines used now have been extracted from natural products that have been part of traditional medicinal practices, and based on this, those natural products are available as registered medicine in the market through pharmacological, chemical studies, and clinical trials (Butler, 2004). This is followed by the extraction and purification of active ingredients from plant metabolites that are found effective in conventional cures. These active metabolites are termed as natural products and have been evidenced as noteworthy candidates in drug discovery programs, which have become an inclusive interdisciplinary field over recent decades (Krüger, 2020). GC–MS, IR, NMR, HPTLC, HPLC, and other high output technologies should be available for the structural interpretation of prudent lead molecules. It will help screen novel molecules by using a computer program and bioinformatics approaches in discovering new drugs from herbal sources. In retrospect, a well-known example of natural product-derived medicine is acetylsalicylic acid, available as aspirin. Acetylsalicylic is the derivative of salicin compound extracted from willow tree Salix alba L. (Der Marderosian and Beutler, 2002). Several medicinally important alkaloids, including morphine, were isolated from opium poppy derived from Papaver somniferum L, and this was another natural product-derived breakthrough in medicine that was commercialized in 1803. Later, in 1870s, codeine, an analgesic, and diacetylmorphine (heroin) were yielded from crude derived-morphine from P. somniferum plant through boiling in acetic anhydride. Traditionally, opium being a sedative agent reported to addict the Arab people. A cardiotonic glycoside, an active constituent of digitoxin derived from Digitalis purpurea L. (foxglove), had been found effective in improving cardiac strength contractibility and enhancement of cardiac conduction. Heart deficiency was found to be treated with the analogs of digitoxins after reporting of its possible long-term detrimental effects and also have therapeutic indications in the management of congestive heart failure (Der Marderosian and Beutler, 2002). The natural product derived from the Cinchona succirubra plant, which was later given the name quinine, was effective against malaria, indigestion, fever, throat diseases, and cancer. C. succirubra was started to be cultivated by the British in the mid-1800s after initial treatment reports. L-Histidine-derived alkaloid, derived from pilocarpine found in Pilocarpus jaborandi (Rutaceae) plant, reported to be effective for the treatment of acute angle-closure glaucoma and chronic open-angle glaucoma for a longer period and approved by FDA in 1994. The oral formulations of pilocarpine are officially prescribed to treat xerostomia, which is characterized by dry mouth as one salivary gland does not make enough saliva. It is also effective in the stimulation of sweat glands to measure sodium and chloride concentrations (De Luca and St Pierre, 2000). Moreover, it was also effective for the treatment of Sjogren’s syndrome, which is an autoimmune disease and also characterized by malfunctioning salivary and lacrimal glands. With such immense importance, natural products have been exploited in both traditional and modern medicines for ages.

1.2.1 Natural products and their historical background

Natural products are biologically active substances originating from natural compounds found in plants, animals, and microorganisms (Baker et al., 2007). The therapeutic uses of natural products started with the use of several herbs that were chewed to relieve pain and use of leaves for healing of wounds as it has been noticed that leaves wrapping on wound areas increase the healing process (Dias et al., 2012). The molecular biology advent coupled with combinatorial chemistry in drug discovery programs made possible the practical uses and commercialization of natural products for prescription. The targeting of any specific protein for inhibiting certain pathways in microorganisms by rational design is the advancement of natural product compounds that came into being like a drug (Li and Lou, 2018). Throughout history, immense knowledge and experience have been accumulated by different civilizations regarding the medicinal potentials of natural products and their broad-spectrum applications in medicine. Retrospectively, the oldest prescription reported in 2600 BC from ancient Mesopotamia was written in ancient Middle East writings on several clay tablets. The poppy seed juice from P. somniferum, cedar oil from Cedrus species, Commiphora myrrha resins, and some other plant-derived substances from almost 1000 plants were described on clay tablets (Newman et al., 2000). From 1550 BC, the Ebers papyrus plant has been seen used frequently by ancient Egyptians. It contains one of the most promising medicinally essential compounds, Ricinus communis, an oil that is used as lactulose to treat stool problems.

Moreover, it also contains Boswellia carteri (frankincense) and Aloe vera (aloe), and almost 700 natural medicinally important agents (Zhong and Wan, 1999). During 460–377 BC, more than 400 natural products were collected by Hippocrates of Cos, which is renowned in Greece. He explored three significant medicinal plants, such as melon juice, Ornithogalum caudatum (squill) juice, and Atropa belladonna extract for relieving constipation, diuretic drug, and anesthesia, respectively. Furthermore, he also described the extraction of Veratrum album (white hellebore) for vomiting and healing (Castiglioni, 1985). During 40–90 AD, De Materia Medica was compiled by Greek physician Pedanius Dioscorides (pharmacologist) and placed the pharmacology foundation in the European region (Wermuth, 2003). De Materia Medica is a medicinal plant pharmacopeia having leaflets of more than 600 plant-derived medicines comprising indications, dosage and administration, precautions, and contraindications. Subsequently, during 129–200 AD, a famed Greek physician and pharmacist named Galen described the harmful ingredients of natural products extracted from herbs as he described almost 600 plant-derived medicines (Cai, 1992). As per initial records, 2600 BC (Mesopotamia), clay tablets exhibit the use of natural products such as oils from Cypress (Cupressus sempervirens) and Myrrh (Commiphora) species. These are still best known for medicinal treatments like cough, cold, and inflammation. The documented records encompass approximately 700 drugs, mostly from medicinal plants, and also include formulas for their usage. Dioscorides recognize some noteworthy medicinal plants in 100 AD, a Greek physician who worked on the assembly, storage, and medicinal plants use.

In contrast, the medicinal herbs were documented by Theophrastus in 300 BC, who was a Greek philosopher and natural scientist. It has been reported that European countries reserved western knowledge during the dark and middle ages. Some of the countries are Germany, England, France, and Ireland, while Arabs retained Greco-Roman knowledge. In the 8th century, the first private pharmacy was owned by Arabs, and various people contributed to this initiative. A pharmacist from France who also was a philosopher, poet, and physician worked together in the development of the first medicine Canon Medicinae. This was the beginning of natural products used as medicine. Gradually the interest in natural products increased due to many influential factors, such as broad-spectrum applications, minimum side effects, and relatively low prices.

1.3 Plants as natural products

Plants and their products, as previously stated, have served as the foundation for traditional medicine systems throughout the world for a long time. The use of plants in different cultures’ traditional medicinal systems is well acknowledged and holds a significant place in the healthcare sector. According to a WHO report, nearly 80% of the population uses traditional medicines as primary care for treatment. In 1820, the first commercial use of natural products started with quinine against malaria, which was isolated from the bark of Cinchona species by French pharmacists. The US FDA later officially endorsed quinine in 2004 against malaria. Other natural products, such as poppy, with analgesic properties were also explored and found to be very effective analgesics. Morphine was derived from the poppy plant by German pharmacist Serturner in 1816.

Moreover, the traditional medicinal plants gave another notable medication, i.e., Rauwolfia serpentina-derived reserpine. This antihypertensive agent reduced elevated high blood pressure and was also utilized in Ayurveda to treat snakebite and other diseases (Cragg and Newman, 2005). The stem and leaves of the Alhagi maurorum Medik plant secrete a sugary and sticky substance. These substances are reported to have broad-spectrum applications in the treatment of various disorders, such as obesity, anorexia, dermatitis, epistaxis, constipation, leprosy, and fever. In addition, it is also used for nutritional purposes as it contains primarily melezitose, sucrose, and invert sugar (Kinghorn et al., 2011). The Salvia plant has considerable importance in medicine for immunity purposes. The hot ashes of the Salvia plant have been frequently used as heat treatment for newborns as immunity-boosting against respiratory pathogens; these babies were considered strongest and healthiest members in their family and tribes. Salvia plant consistently grows in various regions throughout the world, including the US (southwestern region) and Mexico (northwestern), and is used as an aid (Kinghorn et al., 2011). The secretions (gummy sap) of the A. maurorum Medik plant in hot days from stems and leaves are reported to use as Ayurvedic for the treatment of various disorders such as anorexia, obesity, dermatitis, constipation, epistaxis, leprosy, and fever (Dias et al., 2012). Moreover, people in Israel use the extracts of A. maurorum roots to treat bloody diarrhea, and people in Konkan use this plant for asthma treatment.

1.3.1 Antiviral properties of plant-derived natural products

Although natural chemicals are typically employed as unpurified raw extracts, isolating these biomolecules is critical for anticipating their properties linked to pharmacokinetics and pharmacodynamics (absorption, distribution, metabolism, excretion, and toxicity) (Yu and Adedoyin, 2003). Antiviral medications are categorized based on their chemical makeup or their ability to inhibit viral or cellular host protein function. Antiviral action can be exerted in particular due to its ability to impede viral entrance, viral DNA and RNA synthesis, and viral reproduction. Antiviral medications must consider the changes in viral structure and replication cycle (Müller and Kräusslich, 2009). Because of high specific tropism, inhibitors of viral entry and fusion are attracting increased interest for HBV. Methanolic preparations of Hybanthus enneaspermus suppressed HBs Ag binding. Methanolic extracts from Terminalia bellerica seeds and Enicostemma axillare leaves have consistently been demonstrated to inhibit HBV DNA polymerase (Hamza, 2015). Most researchers have recently focused their efforts on designing and testing of synthetic or naturally derived HBs Ag secretion inhibitors. Indeed, in chronic HBV infection, a large amount of HBV surface antigen (HBsAg) release is a primary barrier to HBV elimination. HBeAg and HBsAg secretions into the medium, as well as HBV DNA replication in Hep-G/2.2.15 cells, were considerably suppressed by ethyl acetate and chloroform fractions of Boehmeria nivea leaf extracts, with no cytotoxic effects (Wei et al., 2014). Curcuma longa L extract has been discovered to suppress the transcription of the HBV X (HBx) gene via a p53-mediated route with minimal cytotoxicity in liver cells. Thus far, 219 plants have been reported with a wide variety of antiviral compounds, such as polyphenols that contain hydroxycinnamic acid, hydroxybenzoic acid, flavonoids, stilbenes, and phenols with multiple phenolic rings. The antiviral activity of various plant-derived phenols has been exerted against several life-threatening viruses, including the dengue virus, HIV-1, HIV-2, Marburg virus, Newcastle disease virus (NDV), HBV, and coronaviruses. Multiple mechanisms have been targeted in coronaviruses by using polyphenols-derived antiviral drugs, such as halting of 3-chymotrypsin-like protease (3CLpro), papain-like protease (PLpro) enzymes, and triggering or inhibiting cellular signaling pathways (Annunziata et al., 2020). Previously, a promising antiviral activity has been documented against SARS CoV by various polyphenol compounds isolated from B. papyrifera, such as (30-(3-methylbut-2-enyl)-30, 4-hydroxyisolonchocarpin, broussochalcone A, 4,7-trihydroxyflavane, broussochalcone B, papyriflavonol A, kazinol A, kazinol B, kazinol F, kazinol J, and broussoflavan A). Mpro and RNA-dependent RNA polymerase (RdRp) of SARS CoV-2 are effectively inhibited with polyphenols through in silico analysis. Similarly, higher efficacy of polyphenol was also reported against papain-like protease (PLpro) of SARS-CoV (Bhuiyan et al., 2020). Moreover, the activity of Mpro of SARS CoV-2 has been terminated with flavonoid compounds through in silico studies. Besides polyphenols, several other compounds, most importantly alkaloids and their derivatives, are found with antiviral potential against the influenza virus, HIV-1, DENV, Vesicular Stomatitis Virus, and coronaviruses, including SARS CoV-2. Two alkaloid compounds, 10-hydroxyusambarensine and cryptoquindoline isolated from African medicinal plants, inhibited the Mpro of both SARS coronaviruses (Bhuiyan et al., 2020). At the start of the COVID-19 pandemic, FDA approved the emergency use of chloroquine against SARS CoV-2. Chloroquine is a derivative of alkaloid. Saponins are another plant-derived amphipathic glycosidal compounds with reported antiviral potential against DENV, human (HCR3) rotaviruses, Epstein–Barr virus (EBV), influenza virus, and murine norovirus (MNV). Various isoprene-derived terpenes are reported to be produced by plants that are found with antiviral potential, among which the most important terpenes are monoterpenes, triterpenes, and hemi terpenes (Hussein et al., 2019). Its antiviral activity was reported against dengue virus serotype-1 (DENV-1), bovine viral diarrhea virus, influenza A and B viruses, and previously SARS coronavirus that was reported in 2003. Two triterpenes and sesquiterpenes and ten diterpenes exhibited antiviral activity with IC50 of 3–10 against SARS-CoV and terpene Ginkgolide A strongly inhibit the protease enzyme of SARS CoV-2 (Álvarez et al., 2020). Carissa edulis is a Conkerberry plant that produces various important compounds, most importantly antiviral compounds, and a well-known FDA-approved antiviral drug was isolated from this plant. The higher efficacy of acyclovir was reported against shingles, chickenpox virus, and herpes simplex virus (Bhuiyan et al., 2020).

1.4 Natural products from fungi

Many natural products have been derived from fungi, which have tremendous importance in the medicinal industry. The fungi were recognized with highly profound natural products having extensive spectrum applications in medicine after the first breakthrough of the antibiotic Penicillin by Alexander Fleming in 1929 that resulted from Penicillium fungi (Demain, 2006). Subsequently, various important enzymes and therapeutically active compounds have been derived from fungi (Lorenzen and Anke, 1998). Approximately 75% of polypore fungi studies showed substantial antibacterial activity, suggesting that they could be a useful source for developing new antibiotics. Zjawiony (2004) and Hyde et al. (2019) reported the various fungal substances with anti-cancer, anti-inflammatory, cytotoxic, cardiovascular, immune-stimulating, and antiviral potential. Thus, they are present abundantly. A well-known and frequently used antibiotic, vancomycin, was isolated from Amycolatopsis orientalis fungi as a glycopeptide antibiotic in 1953 and recognized in 1958 for commercial purposes. Vancomycin is reported to be effective against various gram-negative and gram-positive pathogenic bacteria, including Staphylococci, Streptococci, and mycobacteria. Moreover, it is effective against serious bacterial infections and safe in patients allergic to penicillin (Butler, 2004). The development of antibacterial agents from fungal products was a great initiative, and they were safe and associated with fewer side effects than other synthetic antibacterial agents. Recently, the emerging viral infections have threatened human health considerably in the absence of proper antiviral agents and thus scientists are exploring natural products, including fungal-derived natural products, to develop antiviral agents. Two fungal metabolites, mycophenolic acid and cyclosporine A, have been found with antiviral potential against HIV-1 and Vesicular Stomatitis Indiana virus (VSV) and were therefore approved by US FDA as immunosuppressant agents (García-serradilla et al., 2019). The toxicity levels and side effects of mycophenolic acid were reduced by synthesizing its derivatives with diverse functionalities in the aromatic cycle. The Penicillium stoloniferum produces a polysaccharide Statolon that can induce the production of interferon by murine immune cells in response to the infection of Friend Leukemia Virus (Weinhouse, 1962). A patent has been awarded on the fungal compound Statolon for its antiviral properties. The fungal compound verrucarin that is macrocyclic trichothecene mycotoxin is reported to have antiviral properties and anti-cancer properties against lung cancer. It has recently been reported to bind SARS-CoV-2 proteinase in docking studies (Ram et al., 2020). Moreover, VSV25 was inhibited with the antifungal compound Diketopiperazine dimer isolated from Chaetomium cristatumis. Toxicity issues have been found with the antimicrobial compounds in fungi. Still, it is not the limiting factor in the commercialization of fungal compounds, and toxicity level can be minimized by processes of structural simplification and synthesis of derivatives. These examples demonstrate the value of a new insight over the state-of-the-art of research on fungal metabolites with antiviral activity, directed toward the discovery of effective new prescription drugs for individuals infected with SARS-CoV-2 (Aparecida et al., 2021). These studies exhibit the worth of another understanding over the best in the exploration class on antiviral fungal metabolites, coordinated toward the revelation of a compelling new prescription for SARS-COV-2 infection. Moreover, a diverse compound cluster with complex chemical structures has been found in the fungal metabolites. Also, there are some novel compounds, including protease inhibitors and novel antiviral agents, which can be synthesized against SARS-CoV-2 (Suwannarach et al., 2021). The viral transcription and replication are contingent on proteases; thus, proteases are the main target for the drug design of novel antivirals (Aparecida et al., 2021). Fungi with therapeutically and biotechnological importance have been often isolated from terrestrial environments, especially from deep sea, and are believed to be a traditional source. A basic carbon framework (a remarkable α-pyrone pentacyclic) found in brevione F compound isolated from marine fungi has inhibiting potential against HIV replication in vitro in the human leukemia T cell line C8166. Six stereocenters have been reported in the metabolites of the brevione class due to the complex chemical structure that paved the way for the development of a large number of antiviral drugs from this fungal-derived compound (Shishido, 2011). It has been acknowledged that protease inhibitors can be developed from heterocyclic ether present in the skeleton of brevione metabolites. The interaction of fungal metabolites with viral enzyme receptors is enhanced by the O-heterocyclic ring containing strong hydrogen bonds with oxygen. The anti-HIV drugs approved by the FDA, amprenavir and darunavir, contain O-heterocycles (Thorat and Kontham, 2021), thus suggesting their role in the development of antiviral drugs for SARS-CoV-2 infection to control the ongoing pandemic.

1.4.1 Fungal-derived natural products with antiviral potential against SARS-CoV-2

Several FDA-approved antiviral drugs against SARS-CoV-2 have come into view with worldwide efforts to find an effective treatment strategy for the reduction of infection burden and mortality rate. Among these drugs, the majority were isolated from natural products with the focus of interaction with SARS-CoV-2 proteins using molecular docking. The activity of any drug is estimated by molecular docking based on the probability of chemical reactions between drug and viral proteins (Mccammon et al., 2018). New tools have been added to improve the docking programs to increase process reliability and smoothen the way for discovering potential drug leads. Antiviral drugs such as oseltamivir, delavirdine, and ritonavir have been found with a higher affinity for protease of SARS-CoV-2 with the effect of a covalent bond with Cys145 and variable H-bonds.

Similarly, molecular docking also revealed the maximum affinity of etravirine, rilpivirine, and nevirapine for the active site of SARS-CoV-2 protease, wherein compared to HIV protease the affinity was higher for IC50 (half-maximal inhibitory concentration) for SARS-CoV-2 (Mamidala et al., 2020). Preliminary in vitro assays and computational studies revealed several antiviral drugs from natural fungal compounds against SARS-CoV-2 infections (Rao et al., 2020). The fungi C. militaris produces a secondary metabolite known as cordycepin, and a variety of biological functions of this metabolite have been reported, including antiviral, particularly against SARS-CoV-2. It has been reported that it has a high binding affinity to Mpro and binding sites of spike protein, according to the findings of molecular interaction simulations (Verma, 2020). Additionally, cordycepin has a significant similarity to adenosine molecule, suggesting the extra role in blocking of the poly (A) polymerase that is essential for 3′-polyadenylation of viral RNAs like SARS-CoV-2 (Verma, 2020). According to the predictions of the pharmacology network, cordycepin has an association with several biological pathways of viral diseases, encompassing its potential to be repurposed as a novel antiviral drug for COVID-19 treatment (Rao et al., 2020). The Arsenal of candidate molecules produced by fungi having a wide range of antiviral potentials urges consistent endeavors to investigate the capability of these compound libraries in drug discovery programs. The utilization of innovative ways to deal with enhanced metabolic pathways of fungi, programmed pharmacological analysis, molecular docking, and computer-based drug design can help develop a suitable antiviral drug against SARS-CoV-2 (Rao et al., 2020). Fungal metabolites are a promising source for therapeutically important compounds that target the multiple marks (Fig. 1.1) of the viral lifecycle highlighted by various antiviral investigating researches for SARS-CoV-2 infection.

Figure 1.1 The mode of action of natural product-derived antiviral compounds against SARS-CoV-2.

1.5 Structural architecture of SARS-CoV-2

The Coronaviridae family was recognized in 1975 by ICTV (The International Committee on the Taxonomy of Viruses). The members of Coronaviridae are coronaviruses, which are RNA viruses with positive sense, and the genome is non-segmented covered in an envelope, categorized in Nidovirales order (Schoeman and Fielding, 2019). Coronaviridae is the largest family in the Nidovirales order, including two subfamilies; Letovirinae and Orthocoronavirinae. Four genera are classified in Orthocoronavirinae, including delta and gamma coronaviruses that infect birds and alpha and beta coronaviruses that are reported to infect both animals and humans. However, beta coronaviruses have broad tissue tropism and are potentially zoonotic as well; susceptible hosts include humans, bats, and camels (Woo et al., 2007). Beta coronavirus size is approximately 60–140 nm in diameter, and genomic size ranges in 26–32 kb. Likewise, the RNA of newly identified SARS coronavirus-2, isolated in Wuhan from infected patients, comprises almost 29,844 to 29,891 coding nucleotides deficient of the hemagglutinin-esterase gene.

The viral genome is enclosed in a capsid collectively known as the nucleocapsid. The symmetry of nucleocapsid is helically covered in an envelope that protects the viral genome. The envelope is constructed from macromolecules, such as proteins and lipids. These coverings ensure viral safety and protect it from environmental factors influence (Dong et al., 2020). On the envelope spikes, glycoproteins are present that give a crown-like appearance to the viral morphology when observed under an electron microscope. These spiked glycoproteins are essential constituents of the coronavirus that give unique distinctiveness to the virus, thus the ICTV named it coronavirus.

Furthermore, recognizing and binding of the coronavirus to the susceptible host cell is also associated with the role of spiked glycoproteins (Fehr and Perlman, 2015). Glycoproteins with spikes have two domains; one is linked with the part of receptor binding and another has a linkage to the coronavirus envelope. SARS-CoV-2 organizes its genome very wisely, although it is a very short genome enough to use its small genome for multiple functions and its genome codes for the structural and non-structural proteins. Spike (S) proteins, membrane (M), envelope (E), and nucleocapsid (N) are structural proteins, while non-structural proteins (NSPs) are ORF1ab, ORF1ab, ORF1ab, ORF1ab, ORF1ab, ORF1ab, ORF1ab, ORF1ab, ORF1a, and ORF1ab coded by rep gene that makes up around two-thirds of the viral genome (Yang et al., 2020). A wide variety of open reading frames (ORFs) have been discovered in this newly emergent coronavirus. ORFs (ORF1a/b) have been found to encode two out of three sections of the viral genome that translated into two polyproteins named pp1a and pp1ab, which form 16 different NSPs. The structural proteins, such as S proteins, M, E, N, and other auxiliary proteins, are encoded by other ORFs other than ORF1a and b.

Moreover, it also encodes the other accessory proteins that are associated with response to the host innate immune system (Cui et al., 2019). The S2 component is in charge of fusing the viral and host cells (Xia et al., 2014). The S protein of SARS-CoV-2 is one of the most important targets for the development of SARS-CoV-2 vaccines and therapeutics since it is involved in receptor identification, viral attachment, and entry into the host cell (Du et al., 2009). The E protein is necessary for intracellular virus transit and assembly, the M protein for viral assembly and morphogenesis, and the N protein for RNA synthesis (Song et al., 2019). The bat has been recognized as the virus primary host, based on viral genome sequencing, phylogenetic studies, and evolutionary trends, and SARS-CoV-2 may have been transmitted from bats to people via pangolins as an intermediary host. SARS-CoV-2 and Bat-CoV-RaTG13 have 96.2% similar genomic sequences (Guo et al., 2020).

1.6 Epidemiology of SARS CoV-2

The emergence and re-emergence of viral infections, particularly those highly contagious, has been a major public health problem worldwide. At the end of December 2019, the SARS CoV-2 broke out in the Chinese population of Wuhan city, Hubei Province, while representing the impulsive nature of clinical distinctiveness and other associated features. It was difficult to summarize the SARS-CoV-2 origin. Soon, all hospital enrolled and patients were found with epidemiological links to seafood and wet animals in the wholesale market of Wuhan (Zhou et al., 2020). Due to pre-existing epidemiological studies, it was difficult to trace the viral origin and was a question mark for some time; however, a SARS CoV-like virus was identified from bats and was given the name SARS CoV-2. The target site of the SARS-CoV-2 is noticed in the cells of lower airways in a respiratory system, according to the radiological graphs (Li et al., 2020). The ACE2 receptor in humans is mainly expressed in the respiratory tract on which the virus is attached to facilitate the entry of its genetic material into the cell and initiate pathogenesis (Lam et al., 2020). People with a high magnitude of ACE2 receptors are comparatively more vulnerable to COVID-19 disease. The magnitude of the ACE2 receptor might be associated with race. As derived from some scientific theories, the people of Asian countries have a higher expression of ACE2 receptors than white, American, and African (Cyranoski, 2020). Smokers have higher magnitudes of ACE2 receptor cells as they have higher expression of ACE2 gene that significantly increase the risk of infection. Smokers have unfettered ACE2 receptors in altered cell types, although ingredients of cigarettes mediate it; the smoking period and its cession also significantly influence it (Ulhaq et al., 2021). The SARS-CoV-2 enters the lungs through droplet infections from an infected patient. When a virus enters during breathing, it attaches to epithelial cells and binds with ACE2 receptors to penetrate its genetic materials (Emami et al., 2020). According to the SARS CoV laboratory study, primarily, it infects the ciliated cells in the conducting airways. However, due to insufficient innate immunity responses, viral proliferation is started. In this phase, load of the virus is neither adequate nor do disease symptoms appear but still infectious enough and can be diagnosed from nasal secretions. The infants in the age group 45 days to 12 months were positively diagnosed with COVID-19, and noticeably they developed mild symptoms and were not required intensive care (Wu and McGoogan, 2020). According to the WHO report, the prevalence of COVID-19 is less in children, and mostly they are noticed with mild symptoms. In contrast, elders aged 60 and above, especially with already existing diseases, presented severe symptoms with the highest fatality rate. Theoretically, COVID-19 infection ought to be limited to those people who were exposed to the seafood market, and it must have the potential to spread efficiently among humans like another SARS CoV. The first documented case of human-to-human transmission of COVID-19 disease was reported with a cluster of cases in a family. Although they were not experiencing exposure to the Huanan Seafood Market, they still were infected by COVID-19 (Wang et al., 2020a,b). Moreover, the hospital staff and other healthcare officials also reported human-to-human transmission during persistent contact with infected patients. After positive cases among healthcare officials, the isolation ward surfaces and environment of COVID-19 patients were analyzed and were found to be excessively contaminated with SARS-CoV-2 due to coughing and sneezing of infected patients that significantly encourages human-to-human transmission. Meanwhile, analysis of the previous history of hospital-enrolled patients showed that most of them have not been to Huanan Seafood Market in Wuhan. Ultimately, all these cases lead the scientists and health professionals of policymakers to believe SARS-CoV-2 spread from human to human. China and Italy reported the highest transmission cases among healthcare officials, according to reported data (Zhao et al., 2020). Coughing and sneezing that contain respiratory secretions are significantly involved in the transmission of COVID-19, although it is not an airborne disease. Because it has an affinity to land on the ground within 2 m around the affected person because of large droplets instead of remaining suspended in the air. The landed droplets can infect other healthy populations during direct and indirect contact with them. However, the stay duration of landed droplets depends on the type of surface and is significantly mediated by environmental factors like temperatures and humidity (Wan et al., 2020). Besides humans, all living organisms with ACE2 receptor can be infected with SARS-CoV-2. The previous SARS coronavirus was spread through similar route. At the same time, other less common modes of transmission include handling infected animals or source, feco-oral, and fomites, although comparatively, the transmission rates are high in case of SARS-CoV-2. Compared to previous human pathogenic coronavirus, SARS-CoV-2 is noticed with an efficient transmission rate and rapidly spread throughout China and then to the globe after one month of the first outbreak. The nasal secretions were involved in the infection transmission from human-to-human through close contact. In the initial phases of infection after onsets of symptoms, the highest viral load was found in the nasal route, and the virus started spreading through respiratory droplets in 5–6 days of infection, after which a steady flow of virus-containing droplets lead to the transmission rate to peak (Rothe et al., 2020). Moreover, SARS-CoV-2 was also reported in the stool samples of the infected patient. However, there is no official transmission case through stool samples documented in the literature, but detecting SARS-CoV-2 in stool samples suggests that the feco-oral route can potentially transmit it. SARS-CoV-2 is also isolated from serum samples, rectal swabs, urine, and saliva from infected patients, but none reported spreading the virus (Chan et al., 2020a,b). Transmission of SARS-CoV-2 among humans was reported among asymptomatic carriers also, while those asymptomatic carriers have peak viral loads in nasal secretions with no COVID-19 disease symptoms. No COVID-19 disease case of vertical transmission using breastfeeding and sexual intercourse has been reported so far, although an infected mother delivered an infant with abnormal health conditions (Lu et al., 2020). Similarly, no disease case was reported by blood transfusion but still National Blood Center of the National Institute of Health (ISS) actively applies preventive measures during blood transfusion practices. According to the Chinese report, the highest transmission cases, 41%, were reported by humans to humans, healthcare officials reported 29% of cases, 12.3% were family cases, and only 8.7% of the infected population were directly exposed to the potential source (Huanan Fish Market). While during the outbreak of SARS CoV in 2002, the highest transmission rate was observed among health officials (Ong et al., 2020). Till December 2021, SARS-CoV-2 affected 273,685,531 people around the world with 5,357,661 deaths. The highest cases reported were in the US 51,468,453, followed by India 34,726,049, Brazil 22,204,941, United Kingdom 11,190,354, Russia 10,159,389, Turkey 9,136,565, France 8,460,712, Germany 4,745,079, Iran 6,167,650, and Spain 5,455,527 (World Health Organization, 2020 Coronavirus (COVID-19) Dashboard) as shown in Fig.